After investigating this to try to resolve it this weekend, it looks like this is due to the CSS placement being overridden during onshow or applyPlacement: I can manually set the placement:right option in view/stage-logs.js or override the css value for 'top' with onElement.offset().top in the dialog: but when I hit view/widgets/dialog/index.js (IIRC) line 70, the DOM element's explicit inline CSS style for 'top' reverts.
It makes me wonder if the onElement is somehow getting bound to an element other than the stage cell. But in any case, after several hours trying to explain/resolve the behavior, will have to come back to this one.
Probable culprit: https://github.com/jenkinsci/pipeline-stage-view-plugin/blob/master/ui/src/main/js/view/widgets/popover/index.js#L315-L358
The first time this happen to me, I thought the browser had frozen.